neherlab / treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
☆230Updated this week
Alternatives and similar repositories for treetime:
Users that are interested in treetime are comparing it to the libraries listed below
- NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org☆254Updated this week
- breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inte…☆153Updated last month
- A user-friendly workflow for phylogenomics☆204Updated 2 months ago
- snipit: summarise snps relative to your reference sequence☆150Updated last month
- Assembly and intrahost/low-frequency variant calling for viral samples☆128Updated this week
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆118Updated 9 months ago
- Tool to plot synteny and structural rearrangements between genomes☆290Updated 3 weeks ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆308Updated 6 months ago
- BSR-Based Allele Calling Algorithm☆137Updated last month
- Bacterial ribosomal RNA predictor☆230Updated last year
- ☆11Updated last year
- A sequencing simulator☆190Updated 4 months ago
- baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…☆96Updated 2 months ago
- Antimicrobial Resistance Identification By Assembly☆172Updated last year
- Finds SNP sites from a multi-FASTA alignment file☆242Updated 4 years ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆225Updated 10 months ago
- Rapid large-scale prokaryote pan genome analysis☆325Updated 2 years ago
- Build a partitioned pangenome graph from microbial genomes☆244Updated 2 weeks ago
- Pipeline for metabolic annotation of microbial genomes☆142Updated 5 months ago
- Processing pipeline for pan-genome visulization and exploration☆134Updated last year
- Download files from NCBI Entrez by accession☆112Updated 3 months ago
- CAMISIM: Simulating metagenomes and microbial communities☆182Updated 4 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆176Updated last month
- Classifier for metagenomic sequences☆250Updated last month
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆182Updated this week
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆195Updated 3 months ago
- Convert various sequence formats to FASTA☆127Updated 2 years ago
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆233Updated last month
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆110Updated last month
- Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…☆296Updated 4 months ago